Update all plots

BioinfoMachineLearning · Aug 30, 2024 · 3d391bc · 3d391bc
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Showing 30 changed files with 10 additions and 10 deletions.
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_all_multi_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_all_multi_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_all_multi_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_all_multi_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_all_multi_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_all_single_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_all_single_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_all_single_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_all_single_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_all_single_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/casp15_inference_results_plotting.ipynb b/notebooks/casp15_inference_results_plotting.ipynb
@@ -679,7 +679,7 @@
     "        casp15_relaxed_rmsd_lt_2_data_std.fillna(0, inplace=True)\n",
     "\n",
     "        # create the figure and a list of axes\n",
-    "        fig, axis = plt.subplots(figsize=(12, 6))\n",
+    "        fig, axis = plt.subplots(figsize=(18, 8))\n",
     "        axis.spines[\"top\"].set_visible(False)\n",
     "        axis.spines[\"right\"].set_visible(False)\n",
     "        axis.spines[\"bottom\"].set_visible(False)\n",
@@ -738,7 +738,7 @@
     "                \"DynamicBind\",\n",
     "                \"DL-based blind\",\n",
     "                \"NeuralPLexer\",\n",
-    "                \"->  w/o ILCL\",\n",
+    "                \"NeuralPLexer w/o ILCL\",\n",
     "                \"RoseTTAFold-AA\",\n",
     "                \"TULIP\",\n",
     "                \"DiffDock-L-Vina\",\n",
@@ -998,7 +998,7 @@
     "        casp15_relaxed_pb_valid_data_std.fillna(0, inplace=True)\n",
     "\n",
     "        # create the figure and a list of axes\n",
-    "        fig, axis = plt.subplots(figsize=(12, 6))\n",
+    "        fig, axis = plt.subplots(figsize=(18, 8))\n",
     "        axis.spines[\"top\"].set_visible(False)\n",
     "        axis.spines[\"right\"].set_visible(False)\n",
     "        axis.spines[\"bottom\"].set_visible(False)\n",
@@ -1057,7 +1057,7 @@
     "                \"DynamicBind\",\n",
     "                \"DL-based blind\",\n",
     "                \"NeuralPLexer\",\n",
-    "                \"->  w/o ILCL\",\n",
+    "                \"NeuralPLexer w/o ILCL\",\n",
     "                \"RoseTTAFold-AA\",\n",
     "                \"TULIP\",\n",
     "                \"DiffDock-L-Vina\",\n",

diff --git a/notebooks/casp15_method_interaction_analysis.png b/notebooks/casp15_method_interaction_analysis.png
diff --git a/notebooks/casp15_method_interaction_analysis_plotting.ipynb b/notebooks/casp15_method_interaction_analysis_plotting.ipynb
@@ -101,7 +101,7 @@
     "    \"diffdockv1\": \"DiffDock w/o SCT\",\n",
     "    \"dynamicbind\": \"DynamicBind\",\n",
     "    \"neuralplexer\": \"NeuralPLexer\",\n",
-    "    \"neuralplexer_no_ilcl\": \"->  w/o ILCL\",\n",
+    "    \"neuralplexer_no_ilcl\": \"NeuralPLexer w/o ILCL\",\n",
     "    \"rfaa\": \"RoseTTAFold-AA\",\n",
     "    \"tulip\": \"TULIP\",\n",
     "    \"vina_diffdock\": \"DiffDock-L-Vina\",\n",
@@ -423,7 +423,7 @@
     "df = pd.concat(dfs)\n",
     "\n",
     "# plot statistics\n",
-    "fig, axes = plt.subplots(2, 2, figsize=(26, 14), sharey=False)\n",
+    "fig, axes = plt.subplots(2, 2, figsize=(32, 14), sharey=False)\n",
     "\n",
     "interaction_types = [\n",
     "    \"Hydrogen Bond Acceptors\",\n",

diff --git a/notebooks/casp15_public_multi_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_public_multi_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_public_multi_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_public_multi_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_public_multi_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_public_multi_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_public_multi_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_public_multi_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_lddt_pli_violin_plot.png b/notebooks/casp15_public_single_ligand_relaxed_lddt_pli_violin_plot.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_pb_valid_bar_chart.png b/notebooks/casp15_public_single_ligand_relaxed_pb_valid_bar_chart.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_rmsd_lt2_bar_chart.png b/notebooks/casp15_public_single_ligand_relaxed_rmsd_lt2_bar_chart.png
diff --git a/notebooks/casp15_public_single_ligand_relaxed_rmsd_violin_plot.png b/notebooks/casp15_public_single_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/dockgen_inference_results_plotting.ipynb b/notebooks/dockgen_inference_results_plotting.ipynb
@@ -668,7 +668,7 @@
     "dockgen_relaxed_rmsd_lt_2_and_pb_valid_data_std.fillna(0, inplace=True)\n",
     "\n",
     "# create the figure and a list of axes\n",
-    "fig, axis = plt.subplots(figsize=(12, 6))\n",
+    "fig, axis = plt.subplots(figsize=(18, 8))\n",
     "axis.spines[\"top\"].set_visible(False)\n",
     "axis.spines[\"right\"].set_visible(False)\n",
     "axis.spines[\"bottom\"].set_visible(False)\n",

diff --git a/notebooks/dockgen_single_ligand_relaxed_bar_chart.png b/notebooks/dockgen_single_ligand_relaxed_bar_chart.png
diff --git a/notebooks/dockgen_single_ligand_relaxed_rmsd_violin_plot.png b/notebooks/dockgen_single_ligand_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/posebusters_astex_inference_results_plotting.ipynb b/notebooks/posebusters_astex_inference_results_plotting.ipynb
@@ -878,7 +878,7 @@
     "posebusters_rmsd_lt_2_and_pb_valid_data_std.fillna(0, inplace=True)\n",
     "\n",
     "# create the figure and a list of axes\n",
-    "fig, axis = plt.subplots(figsize=(12, 6))\n",
+    "fig, axis = plt.subplots(figsize=(18, 8))\n",
     "axis.spines[\"top\"].set_visible(False)\n",
     "axis.spines[\"right\"].set_visible(False)\n",
     "axis.spines[\"bottom\"].set_visible(False)\n",
@@ -1207,7 +1207,7 @@
     "posebusters_relaxed_rmsd_lt_2_and_pb_valid_data_std.fillna(0, inplace=True)\n",
     "\n",
     "# create the figure and a list of axes\n",
-    "fig, axis = plt.subplots(figsize=(12, 6))\n",
+    "fig, axis = plt.subplots(figsize=(18, 8))\n",
     "axis.spines[\"top\"].set_visible(False)\n",
     "axis.spines[\"right\"].set_visible(False)\n",
     "axis.spines[\"bottom\"].set_visible(False)\n",

diff --git a/notebooks/posebusters_astex_single_ligand_bar_chart.png b/notebooks/posebusters_astex_single_ligand_bar_chart.png
diff --git a/notebooks/posebusters_astex_single_ligand_rmsd_violin_plot.png b/notebooks/posebusters_astex_single_ligand_rmsd_violin_plot.png
diff --git a/notebooks/posebusters_pocket_only_inference_results_plotting.ipynb b/notebooks/posebusters_pocket_only_inference_results_plotting.ipynb
@@ -665,7 +665,7 @@
     "posebusters_relaxed_rmsd_lt_2_and_pb_valid_data_std.fillna(0, inplace=True)\n",
     "\n",
     "# create the figure and a list of axes\n",
-    "fig, axis = plt.subplots(figsize=(12, 6))\n",
+    "fig, axis = plt.subplots(figsize=(18, 8))\n",
     "axis.spines[\"top\"].set_visible(False)\n",
     "axis.spines[\"right\"].set_visible(False)\n",
     "axis.spines[\"bottom\"].set_visible(False)\n",

diff --git a/notebooks/posebusters_single_ligand_pocket_only_relaxed_bar_chart.png b/notebooks/posebusters_single_ligand_pocket_only_relaxed_bar_chart.png
diff --git a/notebooks/posebusters_single_ligand_pocket_only_relaxed_rmsd_violin_plot.png b/notebooks/posebusters_single_ligand_pocket_only_relaxed_rmsd_violin_plot.png
diff --git a/notebooks/posebusters_single_ligand_relaxed_bar_chart.png b/notebooks/posebusters_single_ligand_relaxed_bar_chart.png
diff --git a/notebooks/posebusters_single_ligand_relaxed_rmsd_violin_plot.png b/notebooks/posebusters_single_ligand_relaxed_rmsd_violin_plot.png